Function reference • motus

Download data

tagme(): Download motus tag detections to a database

tellme(): report how much new data motus has for a tag detection database

activity(): Add/update batch activity

metadata(): Update all metadata

nodeData(): Add/update nodeData

activityAll(): Add/update all batch activity

gpsAll(): Add/update all GPS points

Cleaning

Helper functions for cleaning and preparing data

filterByActivity(): Filter alltags by activity

clarify(): report on or claim ambiguous tag detections

deprecateBatches(): Fetch and remove deprecated batches

Helper

getGPS(): Get GPS variables

getRuns(): Returns a dataframe containing runs

simSiteDet(): Create a dataframe of simultaneous detections at multiple sites

sunRiseSet(): Obtain sunrise and sunset times

timeToSunriset(): Obtain time to and from sunrise/sunset for a dataframe containing POSIXct times

sqliteToRDS(): Export results of an sqlite query to an .rds file using limited memory (Linux, OS X; not Windows)

getMotusDBSrc(): Get the src_sqlite for a receiver or tag database

Plotting

plotAllTagsCoord(): Plot all tag detections by latitude or longitude

plotAllTagsSite(): Plot all tag detections by deployment

plotDailySiteSum(): Plots number of detections and tags, daily, for a specified site

plotRouteMap(): Map of tag routes and sites coloured by id

plotSite(): Plot all tags by site

plotSiteSig(): Plot signal strength of all tags by a specified site

plotTagSig(): Plot signal strength of all detections for a specified tag by site

Summarizing

siteSum(): Summarize and plot detections of all tags by site

siteSumDaily(): Summarize daily detections of all tags by site

siteTrans(): Summarize transitions between sites for each tag

tagSum(): General summary of detections for each tag

tagSumSite(): Summarize detections of all tags by site

Filtering

Functions for creating database filters

getRunsFilters(): Find runFilters

listRunsFilters(): Returns a dataframe of the filters stored in the local database.

createRunsFilter(): Create a new filter records that can be applied to runs

deleteRunsFilter(): Delete a filter matching a filter name (and optionally a project ID)

writeRunsFilter(): Write to the local database the probabilities associated with runs for a filter

Administration

getAccess(): Return accessible projects and receivers

motusLogout(): Forget login credentials for motus.

checkVersion(): Verifies the version of the package against the admInfo table of a motus file. Those should match if the updateMotusDb function has been properly loaded by the tagme function.